the first commit

dir_util.py

@@ -0,0 +1,91 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+import os
+
+from flask_api import status
+
+import env
+from cellxgene_exception import CellxgeneException
+
+
+def is_subdir(full_path, parent_path):
+    subdir = os.path.realpath(full_path)
+    parent = os.path.realpath(parent_path)
+    return subdir.startswith(parent)
+
+
+def create_dir(parent_path, dir_name):
+    full_path = os.path.join(parent_path, dir_name)
+
+    if "/" in dir_name:
+        raise CellxgeneException(
+            "Please have no slashes in the intended directory.",
+            status.HTTP_400_BAD_REQUEST,
+        )
+    elif not os.path.exists(parent_path):
+        raise CellxgeneException(
+            "The selected User directory does not exist.", status.HTTP_400_BAD_REQUEST
+        )
+    elif os.path.exists(full_path):
+        raise CellxgeneException(
+            "The provided subdirectory already exists within Directory.",
+            status.HTTP_400_BAD_REQUEST,
+        )
+    elif not is_subdir(full_path, parent_path):
+        raise CellxgeneException(
+            "The directory must be a subdirectory of the parent path.",
+            status.HTTP_400_BAD_REQUEST,
+        )
+    elif not os.path.isdir(parent_path):
+        raise CellxgeneException(
+            "The parent is not a directory.", status.HTTP_400_BAD_REQUEST
+        )
+    else:
+        os.mkdir(full_path)
+
+
+def recurse_dir(path):
+    if not os.path.exists(path):
+        raise CellxgeneException(
+            "The given path does not exist.", status.HTTP_400_BAD_REQUEST
+        )
+
+    def make_entry(el):
+        full_path = os.path.join(path, el)
+        if os.path.isfile(full_path):
+            return {
+                "path": full_path.replace(env.cellxgene_data, ""),
+                "name": el,
+                "type": "file",
+            }
+        elif os.path.isdir(full_path):
+            return {
+                "path": full_path,
+                "name": el,
+                "type": "directory",
+                "children": recurse_dir(full_path),
+            }
+        else:
+            raise CellxgeneException(
+                "Given path is neither file nor directory.", status.HTTP_400_BAD_REQUEST
+            )
+
+    return [make_entry(x) for x in os.listdir(path)]
+
+
+def render_entries(entries):
+    return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
+
+
+def render_entry(entry):
+    if entry["type"] == "file":
+        return f"<li> <a target='_blank' href='view{entry['path']}'>{entry['name']}</a></li>"
+    elif entry["type"] == "directory":
+        return f"<li>{entry['name']}{render_entries(entry['children'])}</li>"